Advertisement

Tree Genetics & Genomes

, 11:1 | Cite as

The genetic diversity and introgression of Juglans regia and Juglans sigillata in Tibet as revealed by SSR markers

  • Hua Wang
  • Gang Pan
  • Qingguo Ma
  • Junpei Zhang
  • Dong PeiEmail author
Original Paper

Abstract

While walnuts are grown worldwide, two species are predominantly cultivated in China, Juglans regia and Juglans sigillata. J. regia is a widespread species, while J. sigillata is an indigenous species mainly distributed in southwestern China. In Tibet, unique plateau climatic conditions and relatively low-intensity agriculture aid walnuts to preserve a great variety of genetic resources. Knowing the genetic diversity and genetic structure of walnut populations in Tibet is essential when planning genetic conservation and screening for superior germplasm resources. The objectives of this study were to reveal the genetic diversity and genetic structure of walnut populations in Tibet and to infer the relationship between two species, J. regia and J. sigillata, using 12 molecular markers. The results based on screening 209 walnut trees from nine populations showed that the level of polymorphism is moderately high. However, the number of rare alleles (allele frequency <0.05) was higher than that reported in previous studies. An analysis of molecular variance revealed that significant genetic variation existed both among populations of J. regia (10.25 %, p < 0.0001) and J. sigillata (11.07 %, p < 0.0001) and between the two species (7.91 %, p < 0.0001). A Bayesian approach divided the 209 walnut samples into two clusters and presented the differentiation pattern of these two species. The assignment analysis revealed the presence of J. regia × J. sigillata hybrids among the sampled individuals. The results suggest unique germplasm preservation among the walnut populations in Tibet and that introgression between J. regia and J. sigillata may account for the convoluted boundary between the two species.

Keywords

Genetic diversity Genetic structure Juglans sigillata Juglans regia SSR Introgression Tibet 

Notes

Acknowledgments

The authors thank Zheng Weilie (Tibet Institute of Agriculture and Animal Husbandry, Linzhi) for logistical help and Dr. Ma Heping and Bianbaduoji (Tibet Institute of Agriculture and Animal Husbandry, Linzhi) for assistance with sampling. We warmly thank the crew from the local District Forestry Bureau for providing information of local walnut resources and assisting with sampling, and the local Tibetan people for their hospitality and help in sample collecting. We also thank Zeng Yanfei (the Chinese Academy of Forestry, Beijing) for her support in data analysis. Financial support was received from the National Science & Technology Pillar Program (2013BAD14B01) and from the National Natural Science Foundation of China (31400558).

Data Archiving Statement

The raw data of this research was submitted to the TreeGenes Database. The accession numbers of genotypes and environmental descriptors of Juglans sigillata and J. regia are under TGDR029 and TGDR030, respectively.

Supplementary material

11295_2014_804_MOESM1_ESM.docx (19 kb)
ESM 1 (DOCX 18 kb)

References

  1. Aradhya M, Potter D, Simon C (2004) Origin, evolution, and biogeography of Juglans: a phylogenetic perspective. V Int Walnut Symp 705:85–94Google Scholar
  2. Bagnoli F, Vendramin G, Buonamici A, Doulis A, Gonzalez-Martinez SC, La Porta N, Magri D, Raddi P, Sebastiani F, Fineschi S (2009) Is Cupressus sempervirens native in Italy? An answer from genetic and palaeobotanical data. Mol Ecol 18:2276–2286CrossRefPubMedGoogle Scholar
  3. Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165CrossRefPubMedGoogle Scholar
  4. Bayazit S, Kazan K, Gulbitti S, Cevik V, Ayanoglu H, Ergul A (2007) AFLP analysis of genetic diversity in low chill requiring walnut (Juglans regia L.) genotypes from Hatay, Turkey. Sci Hortic 111:394–398CrossRefGoogle Scholar
  5. Christopoulos MV, Rouskas D, Tsantili E, Bebeli PJ (2010) Germplasm diversity and genetic relationships among walnut (Juglans regia L.) cultivars and Greek local selections revealed by Inter-Simple Sequence Repeat (ISSR) markers. Sci Hortic 125:584–592. doi: 10.1016/j.scienta.2010.05.006 CrossRefGoogle Scholar
  6. Ciarmiello LF, Pontecorvo G, Piccirillo P, Luca A, Carillo P, Kafantaris I, Woodrow P (2013) Use of nuclear and mitochondrial single nucleotide polymorphisms to characterize english walnut (Juglans regia L.) genotypes. Plant Mol Biol Rep 31:1116–1130. doi: 10.1007/s11105-013 -0575-2 CrossRefGoogle Scholar
  7. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014PubMedCentralPubMedGoogle Scholar
  8. Dangl GS, Woeste K, Aradhya MK, Koehmstedt A, Simon C, Potter D, Leslie CA, McGranahan G (2005) Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut. J Am Soc Hortic Scie 130:348–354Google Scholar
  9. Duan S (1984) The investigation of walnut originating in Tibet. Acta Horticult Sinica 11:231–234 (in Chinese)Google Scholar
  10. Ebrahimi A, Fatahi R, Zamani Z (2011) Analysis of genetic diversity among some Persian walnut genotypes (Juglans regia L.) using morphological traits and SSRs markers. Sci Hortic 130:146–151. doi: 10.1016/j.scienta.2011.06.028 CrossRefGoogle Scholar
  11. Erturk U, Dalkilic Z (2011) Determination of genetic relationship among some walnut (Juglans regia L.) genotypes and their early-bearing progenies using RAPD markers. Rom Biotechnol Lett 16:5944–5952Google Scholar
  12. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620. doi: 10.1111/j.1365-294 CrossRefPubMedGoogle Scholar
  13. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567CrossRefPubMedGoogle Scholar
  14. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedCentralPubMedGoogle Scholar
  15. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578CrossRefPubMedCentralPubMedGoogle Scholar
  16. Fan ZY, Fang WL, Dong RQ (2005) Comparison and selection of pollinated Biyangpao walnut varieties. South China Fruits 34:58–59 (in Chinese)Google Scholar
  17. Fatahi R, Ebrahimi A, Zamani Z (2010) Characterization of some Iranians and foreign walnut genotypes using morphological traits and RAPD markers. Hortic Environ Biotechnol 51:51–60Google Scholar
  18. Fjellstrom RG, Parfitt DE (1994) Walnut (Juglans spp.) genetic diversity determined by restriction fragment length polymorphisms. Genome 37:690–700CrossRefPubMedGoogle Scholar
  19. Fornari B, Malvolti ME, Taurchini D (2001) Isozyme and organellar DNA analysis of genetic diversity in natural/naturalised European and Asiatic walnut (Juglans regia L.) populations. Acta Horticult Sci 544:167–178Google Scholar
  20. Garza J, Williamson E (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318CrossRefPubMedGoogle Scholar
  21. Glaubitz JC (2004) CONVERT: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol Notes 4:309–310CrossRefGoogle Scholar
  22. Gleeson SK (1982) Heterodichogamy in walnuts: inheritance and stable ratios. Evolution 36:892–902CrossRefGoogle Scholar
  23. Gunn BF, Aradhya M, Salick JM, Miller AJ, Yongping Y, Lin L, Xian H (2010) Genetic variation in walnuts (Juglans regia and J. sigillata; Juglandaceae): species distinctions, human impacts, and the conservation of agrobiodiversity in Yunnan, China. Am J Bot 97:660–671. doi: 10.3732/ajb.0900114 CrossRefPubMedGoogle Scholar
  24. Jarvis DI, Brown AHD, Cuong PH, Collado-Panduro L, Latournerie-Moreno L, Gyawali S, Tanto T, Sawadogo M, Mar I, Sadiki M, Hue NTN, Arias-Reyes L, Balma D, Bajracharya J, Castillo F, Rijal D, Belqadi L, Rana R, Saidi S, Ouedraogo J, Zangre R, Rhrib K, Chavez JL, Schoen D, Sthapit B, De Santis P, Fadda C, Hodgkin T (2008) A global perspective of the richness and evenness of traditional crop-variety diversity maintained by farming communities. Proc Natl Acad Sci U S A 105:5326–5331. doi: 10.1073/pnas.0803431105 CrossRefPubMedCentralPubMedGoogle Scholar
  25. Karimi R, Ershadi A, Vahdati K, Woeste K (2010) Molecular characterization of Persian walnut populations in Iran with microsatellite markers. Hortscience 45:1403–1406Google Scholar
  26. Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738PubMedCentralPubMedGoogle Scholar
  27. Krüssmann G, Epp ME, Daniels GS (1985) Manual of cultivated broad-leaved trees & shrubs, Volume II, E-PRO. Timber Press/American Horticultural SocietyGoogle Scholar
  28. Kuang KZ, Lu AM (1997) Flora of China, vol 21. Science Press, Beijing, China:33–36 (in Chinese)Google Scholar
  29. Ladizinsky G (1985) Founder effect in crop-plant evolution. Econ Bot 39:191–199CrossRefGoogle Scholar
  30. Levene H (1949) On a matching problem arising in genetics. Ann Math Stat 20:91–94CrossRefGoogle Scholar
  31. Ma QG, Zhang JP, Pei D (2011) Genetic analysis of walnut cultivars in China using fluorescent amplified fragment length polymorphism. J Am Soc Hortic Sci 136:422–428Google Scholar
  32. Manning WE (1978) The classification within the Juglandaceae. Ann Mo Bot Gard 65:1058–1087CrossRefGoogle Scholar
  33. Martin MA, Mattioni C, Cherubini M, Taurchini D, Villani F (2010) Genetic diversity in European chestnut populations by means of genomic and genic microsatellite markers. Tree Genetics Genomes 6:735–744CrossRefGoogle Scholar
  34. Miller AJ, Schaal BA (2006) Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae). Mol Ecol 15:1467–1480. doi: 10.1111/j.1365-294×.2006.02834.× CrossRefPubMedGoogle Scholar
  35. Mitchell-Olds T, Willis JH, Goldstein DB (2007) Which evolutionary processes influence natural genetic variation for phenotypic traits? Nat Rev Genet 8:845–856CrossRefPubMedGoogle Scholar
  36. Nei M (1972) Genetic distance between populations. Am Nat 106:283–292CrossRefGoogle Scholar
  37. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A 70:3321–3323CrossRefPubMedCentralPubMedGoogle Scholar
  38. Oosterhout CV, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  39. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  40. Pollegioni P, Woeste K, Mugnozza GS, Malvolti ME (2009) Retrospective identification of hybridogenic walnut plants by SSR fingerprinting and parentage analysis. Mol Breed 24:321–335. doi: 10.1007/s11032-009-9294-7 CrossRefGoogle Scholar
  41. Pollegioni P, Woeste K, Olimpieri I, Marandola D, Cannata F, Malvolti ME (2011) Long-term human impacts on genetic structure of Italian walnut inferred by SSR markers. Tree Genetics Genomes 7:707–723. doi: 10.1007/s11295-011-0368-4 CrossRefGoogle Scholar
  42. Pollegioni P, Olimpieri I, Woeste KE, Simoni G, Gras M, Malvolti ME (2012) Barriers to interspecific hybridization between Juglans nigra L. and J. regia L species. Tree Genetics Genomes 9:291–305. doi: 10.1007/s11295-012-0555-y CrossRefGoogle Scholar
  43. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  44. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228PubMedCentralPubMedGoogle Scholar
  45. Takezaki N, Nei M, Tamura K (2010) POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 27:747–752CrossRefPubMedCentralPubMedGoogle Scholar
  46. Victory ER, Glaubitz JC, Rhodes OE, Woeste KE (2006) Genetic homogeneity in Juglans nigra (Juglandaceae) at nuclear microsatellites. Am J Bot 93:118–126CrossRefGoogle Scholar
  47. Wang H, Pei D, Gu RS, Wang BQ (2008) Genetic diversity and structure of walnut populations in central and southwestern China revealed by microsatellite markers. J Am Soc Hortic Sci 133:197–203Google Scholar
  48. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  49. Woeste K, Burns R, Rhodes O, Michler C (2002) Thirty polymorphic nuclear microsatellite loci from black walnut. J Hered 93:58–60CrossRefPubMedGoogle Scholar
  50. Xi RT, Zhang YP (1996) Fruit trees of China. Walnut Chinese Forestry Press, Beijing (in Chinese)Google Scholar
  51. Yen F, Yang R, Mao J, Ye Z, Boyle T (1997) POPGENE, the Microsoft Windows-based user-friendly software for population genetic analysis of co-dominant and dominant markers and quantitative traits. Dept Renewable Resources, University of Alberta, EdmontonGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Hua Wang
    • 1
    • 2
  • Gang Pan
    • 3
  • Qingguo Ma
    • 2
  • Junpei Zhang
    • 2
  • Dong Pei
    • 2
    Email author
  1. 1.Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanPeople’s Republic of China
  2. 2.Key Laboratory of Silviculture, The Institute of ForestryThe Chinese Academy of ForestryBeijingPeople’s Republic of China
  3. 3.Agricultural and Animal Husbandry Collage of Tibet UniversityLinzhiPeople’s Republic of China

Personalised recommendations